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ANCILLARY SCIENTISTS SYMPOSIUM |
Roslin Institute, Edinburgh, Midlothian EH25 9PS, United Kingdom
2 Corresponding author: dave.burt{at}bbsrc.ac.uk
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONCHICKEN GENOMEIMPLICATIONS OF THE CHICKEN...CONCLUSIONS AND FUTURE PROSPECTSREFERENCES |
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Key Words: chicken • genome • database • quantitative trait loci • evolution
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONCHICKEN GENOMEIMPLICATIONS OF THE CHICKEN...CONCLUSIONS AND FUTURE PROSPECTSREFERENCES |
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The Era of Chicken Genomics
The modern era of avian genomics can be traced to the development of the genetic linkage maps based on molecular markers in the mid-1990s (Proceedings of the 23rd Conference of the International Society for Animal Genetics, 1992). The first were based on the Compton (Bumstead and Palyga, 1992) and East Lansing (Levin et al., 1994) reference mapping populations. The driving force for developing these maps was the desire to perform whole genome linkage studies using thousands of markers to map QTL. This was made possible using markers more suited to high-throughput methods, such as those based on microsatellite sequences (Cheng et al., 1995). From an analysis of markers used across several mapping populations, a consensus map of over 2,000 loci, spanning 4,000 cM, was constructed (Groenen and Crooijmans, 2003).
The creation of comparative maps between the gene-poor maps of the chicken with the gene-rich map of human was at first seen as the only realistic way of predicting the gene content of QTL. Comparative maps between the chicken and mammals were used to trace the origin of avian sex chromosomes from a pair of autosomes (Fridolfsson et al., 1998; Nanda et al., 1999). A comprehensive analysis of gene mapping data was used to reveal extensive conservation of synteny between chicken and mammals (Burt et al., 1999). This conclusion was confirmed and extended by analysis of sequences of vertebrate genomes (Hillier et al., 2004; Bourque et al., 2005).
Physical mapping of genes by cytogenetic techniques has been used to complement genetic mapping approaches. The chicken genome has a haploid content of 1.1 x 109 bp of DNA and is divided among 39 chromosomes including 9 pairs of cytologically distinct macrochromosomes and 30 microchromosomes (Ladjali-Mohammedi et al., 1999). The 30 chicken microchromosomes contain about one-third of the genomic DNA but are gene-rich, with estimates suggesting that microchromosomes contain at least twice as many genes as the macrochromosomes (McQueen et al., 1996; Smith et al., 2000); again, this has been confirmed and extended by the analysis of the chicken genome sequence (Hillier et al., 2004). Isolation of genomic clones [mostly in bacterial artificial chromosome (BAC) cloning vectors] and individual microchromosomes by microdissection has created a universal set of DNA probes or so-called landmark probes specific for each chromosome (Masabanda et al., 2004). It is now relatively simple to map any cloned gene to a specific chromosome, even a microchromosome using 2-color fluorescent in situ hybridization using these probes to create integrated genetic and physical maps of macro-and microchromosomes (Schmid et al., 2005).
A major limitation of genetic markers for the construction of gene maps has been the need to identify polymorphisms, necessary to track their inheritance in linkage studies. The use of radiation hybrid (RH) mapping panels to construct gene maps of many other species has increased the rate of gene mapping significantly. In this method, the presence or absence of a marker is only required (usually based on a PCR assay), and there is no need to identify polymorphisms. A chicken RH panel (Morisson et al., 2003) has been used to construct maps of chromosomes 2, 7, 14, and 15, which are colinear with the genetic map (Morisson et al., 2003, 2005; Jennen et al., 2004; Leroux et al., 2005).
Physical mapping has now moved beyond cytogenetic mapping with the creation of complete physical maps of the chicken genome based on large BAC clones (Ren et al., 2003). Bacterial artificial chromosome libraries have been constructed from a White Leghorn line (Crooijmans et al., 2000) and an inbred Jungle Fowl line (Lee et al., 2003) used in the chicken genome sequencing project. The Washington University Genome Sequencing Center (htt p://genome.wustl.edu/genome.cgi?GENOME=Gallus %20gallus) has fingerprinted over 188,000 BAC clones from many of these libraries and has constructed a BAC physical map of 260 contigs based on over 143,000 BAC fingerprints. Over 75% (202/260 contigs) of the BAC contigs have been anchored to a chromosome mostly by the work of Romanov et al. (2003) using an oligonucleotide hybridization strategy. The development of the chicken BAC map has been an important step in the assembly of the chicken genome sequence (Wallis et al., 2004).
Sequencing analysis in the chicken reached a new level with the characterization of more than 500,000 sequenced EST (Abdrakhmanov et al., 2000; Tirunagaru et al., 2000; Boardman et al., 2002). This has been followed by many other EST projects with 599,330 EST in the current release of dbEST (011907). These studies have been extended with the full-length sequencing of 17,000 cDNA (Hubbard et al., 2005; Caldwell et al., 2005). Recently, Fred Leung created a database for full-length cDNA in the chicken (Wang et al., 2007; http://www.bioinfo.hku.hk/chicken/). These EST resources were used to create cDNA microarrays for high throughput gene expression studies (Cogburn et al., 2003; van Hemert et al., 2003; Burnside et al., 2005; Ellestad et al., 2006; Ruby et al., 2006; Smith et al., 2006). Later, these EST resources were used together with gene predictions based on the genome sequence to design a 20K oligoarray (www.ark-genomics.co.uk) and DNA chips (www.affymetrix.com) for whole-genome gene expression studies.
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CHICKEN GENOME |
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TOPABSTRACTINTRODUCTIONCHICKEN GENOMEIMPLICATIONS OF THE CHICKEN...CONCLUSIONS AND FUTURE PROSPECTSREFERENCES |
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50% found in mammals. A 6.6-fold coverage of the genome was produced using the DNA from a single inbred female Jungle Fowl. This line was 1 of the 2 inbred lines used to generate the reference East Lansing back-cross mapping population (Levin et al., 1994). In addition, a BAC library was constructed from this line as part of the BAC physical mapping project (Wallis et al., 2004). Together with the genetic and physical maps of the chicken (Schmid et al., 2005), 32,767 supercontigs were assembled into a scaffold of 933 Mb or 89% of the estimated 1,050-Mb genome. The female is the heterogametic sex in birds, with single copies of the Z and W chromosomes. Consequently, these chromosomes were poorly represented in the final assembly. Unlike the rest of the genome, the W chromosome has a high repeat content, impossible to assemble to any great extent using the whole genome sequencing approach, with only about 260 Kb in the final assembly. Consequently, targeted sequencing of these sex chromosomes will be necessary to complete their assembly, currently underway at the Massachusetts Institute of Technology (S. Rozen, personal communication). Therefore in 2006, additional data from 250,000 targeted sequencing reads were integrated with more extensive genetic and physical maps to produce a second assembly WASHU2.
The new version has resolved many errors, in particular the assembly of the sex chromosome Z, which has increased from 34 to 75 Mb. This was made possible by integrating results from genetic, RH, and BAC maps, as well as other experimental data on cDNA genes (Figure 1
). The assembly now contains 16,775 supercontigs of 1,030 Mb or 98% of total genome. More contigs have been assigned to specific chromosomes (86.1 vs. 94.6%) and consequently fewer assignments to Chr*_random (2.4 vs. 0.3%) and ChrUn (11.5 vs. 5.1%). This used data from overgo (Romanov et al., 2003) and FISH mapping of specific BAC clones (Masabanda et al., 2004; D. Griffin, University of Kent, Centerbury, UK, unpublished data). Still to be resolved are the smallest microchromosomes, 29, 30, 31, 33, 34, 35, 36, 37 and 38, still unassigned to any sequenced contigs. Sequence data is available for the linkage groups E64, E22C19W28, and E50C23, which are likely to be assigned to these smallest microchromosomes. Gene coverage for WASHU2 was estimated to be 95% based on an overlap with available cDNA clones. During the next few years, we can expect more improvements in the chicken genome assembly with more targeted sequencing of the W chromosome and sequence assignment to the smaller microchromosomes.
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Gene Function of Known and Predicted Chicken Genes
The Gene Ontology (GO; http://www.geneontology.org/) is an international resource for gene annotation used by bioinformatics and functional genomics communities. Currently, there are 22,625 GO terms used to describe attributes of gene products in many of the well-known model organism and genome annotation groups. The GO consists of 3 structured vocabularies that focus on computational representations of concepts in molecular biology in which there are semantic understandings that are widely shared. These vocabularies are molecular function (what action a gene product performs), biological process (biological goal accomplished by 1 or more ordered assemblies of molecular functions), and cellular component (subcellular location of action or macromolecular complexes). The annotation of chicken genes is in its infancy, with most GO terms being assigned by in silico methods. At present, there are 16,113 chicken proteins that have GO annotation (http://www.ebi.ac.uk/GOA/). Of these, 98% have been assigned electronically and only 2% assigned through high-quality manual GO curation. This compares with 32 and 45% for human and mouse, respectively. The creation of the chicken GO consortium (currently only AgBase, http://www.agbase.msstate.edu/, is funded for high quality but labor intensive manual curation and GO annotation for automated annotation) is an effort to overcome these problems and tap into a rich seam of biological knowledge on vertebrate gene function. For those interested in helping, contact the farm animal gene ontology mailing list (www.geneontology.org/GO.list.farmanimals.shtml).
Information on gene function from model organisms and human to orthologs in the chicken has provided important clues to their role in birds. In recent years, there have been many new tools and databases providing lists of orthologs between chicken and other species. New databases include Compara (http://www.ensembl.org/), OrthoMCL (http://orthomcl.cbil.upenn.edu/), InParanoid (http://inparanoid.sbc.su.se/), and Metazome (http://www.metazome.net/); besides sequence homology, information based on phylogenetic trees and conservation of gene order is also used to infer gene orthology vs. gene paralogy. For the Ensembl 42 gene set, 13,000 chicken genes have an orthologs with 15,000 human genes in the Compara database. This either suggests that there have been more gene duplication events in the mammalian lineage or more gene losses in the avian lineage. Comparison of vertebrate genes suggests a mixed model of gene gains:gene losses (Hillier et al., 2004).
The availability of the chicken genome and a predicted genome-wide set of genes provides new opportunities for whole genome-based gene association and gene expression-based investigations. The chicken genome project has generated many new resources and experimental tools such as whole genome gene expression arrays, full-length cDNA clones, etc. for studies of gene function (see www.ark-genomics.org). Gene annotation, for example, using the gene ontologies is critical to make sense of these studies. Besides information on specific genes, these analyses also require knowledge of the role of many genes in specific biochemical and signaling pathways. In recent years, there has been an increase in knowledge in this area with new databases and tools for further analysis (Reactome, www.reactome.org/; GenMAPP, www.genmapp.org/; KEGG, www.genome.jp/kegg/pathway.html; and GallusKB, udgenome.ags.udel.edu/gallus/). At this stage, pathway information in the chicken is mostly inferred using orthology relations between chicken and human genes, again another area for improvement.
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IMPLICATIONS OF THE CHICKEN GENOME PROJECT |
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TOPABSTRACTINTRODUCTIONCHICKEN GENOMEIMPLICATIONS OF THE CHICKEN...CONCLUSIONS AND FUTURE PROSPECTSREFERENCES |
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310 million years ago (Hedges, 2002). Sequence comparisons among these groups are characterized by a high signal-to-noise ratio for the detection of conserved, presumably functional elements. Taken together with the ready access to chicken embryos and as a major food source, chicken genomics is likely to have major applications and benefits in comparative genomics, evolutionary biology and systematics, models of development and human disease, and agriculture.
Implications for Agriculture
In the current version of dbSNP (Build 126), there are 2,970,811 entries for chicken single nucleotide polymorphisms (SNP), and most were generated by a consortium led by the Beijing Genome Institute (Wong et al., 2004; Wang et al., 2005). These SNP were identified from a comparison of shotgun sequences from Silkie, broiler, and layer chicken lines with the Red Jungle Fowl as reference. Resequencing confirmed 94% of SNP and 83% of the non-synonymous coding SNP. In addition, 70% of SNP were common to all breeds examined and suggested an origin before the domestication of poultry 10,000 yr ago. Another possibility could be that the ancestry of these samples has been lost due to extensive cross-breeding between Asian and Western poultry populations. However, the segregation of large numbers of common SNP between and within broiler and layer populations provides information on a large number of potential genetic markers for QTL mapping in poultry. Recently, cost-effective solutions for typing 10,000 or more SNP have become available (www.illumina.com; www.affymetrix.com). When combined with the ease of building large resource populations, these developments hold much promise toward the identification of genes controlling quantitative traits in poultry (Figure 2).
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400 gene associations. These early collaborations have highlighted many problems and issues relating to QTL data. First, to encourage data sharing, it is necessary to agree on standards for describing QTL data. These should include data on the QTL description (trait name, age, chromosome, position, flanking markers, significance, QTL effects on the trait, etc.), parameters of the study (type of cross, number of animals in the study, breed or line description, statistic or software used, etc.), and published references. Also, how are traits to be described? It is clear that we need to agree on a trait ontology (a standard vocabulary) from which poultry traits can be described. In the future, we hope adopting such strategies and standards will facilitate new analyses, for example, comparative mapping of QTL between species as diverse as chicken and pigs.
Implications for Medicine
The chicken as a model for human eye defects is used as an example of its use in medical research. Five chicken mutants have been used as models of retinal degeneration. A candidate gene study defined the defect in retinal degeneration as a null mutation in the photoreceptor guanylate cyclase (Semple-Rowland et al., 1998). Other blind defects include blindness enlarged globe (Pollock et al., 1982), sex-linked retinal dysplasia and degeneration (Randall et al., 1983), delayed amelanotic strain DAM8 (Komenda and Fite, 1983), and retinopathy globe enlarged (RGE; Montiani-Ferreira et al., 2005). Recently, we mapped and characterized the genetic defect in RGE using the tools of genomics (Inglehearn et al., 2003; Tummala et al., 2006). Using microsatellite markers, a whole genome genetic scan mapped RGE to the short arm of chicken chromosome 1. Examination of the confidence interval, using the Ensembl genome browser, highlighted many candidate genes—the most promising being G nucleotide-binding protein-ß3 (GNB3). This gene encodes a cone transducin ß subunit. Isolation and sequencing of GNB3 cDNA from RGE and wild-type chicks identified an in-frame 3-bp deletion that removes a single aspartic residue. Further alignment of GNB3 sequences from other vertebrates showed that the RGE mutation deletes a highly conserved Asp residue in the third of 7 WD repeat domains in GNB3. The WD proteins are made up of highly conserved repeating units usually ending with Trp-Asp (WD). They are found in all eukaryotes but not in prokaryotes. They regulate cellular functions, such as cell division, cell-fate determination, gene transcription, transmembrane signaling, mRNA modification, and vesicle fusion (Neer et al., 1994). In silico protein modeling suggests that the RGE mutation destabilizes the GNB3 protein. It also removes ß sheets propellers 1 and 5, important for transducin activity. A 70% reduction in immunoreactivity to anti-GNB3 in RGE-affected retinas confirmed this prediction and verified the gene defect. Recently, we mapped the genetic defect in retinal dysplasia and degeneration (Burt et al., 2003), and using the same approach described above will identify the molecular defect.
Implications for Fundamental Biology
The chicken has been used as a model in developmental biology for over 100 yr (Stern, 2005). The example described here is the use of the chick limb bud to understand cell patterning during development. Classic grafting experiments (Tickle et al., 1975) of posterior regions of the limb bid to the anterior region generated mirror duplications of the digit pattern. Further studies over many decades defined many aspects of this polarizing region. In particular, a molecule sonic hedgehog (SHH) homologous to a gene found in Drosophila was identified as a major component of the polarizing region. The SHH pathway has a role to play in the development of many organs, including the limb, nervous system, face, gut, lung, teeth, hair or feathers, and biological processes: hematopoiesis, vasculogenesis, angiogenesis, etc. So it is not surprising that genetic defects in this pathway cause many disorders and syndromes, including holoprosencephaly, gut and lung malformations, as well as many cancers, such as medulloblastoma, basal cell carcinoma, glioblastoma, and forms of prostate cancer.
The SHH signaling pathway is complex and consists of a family of ligands related to hedgehog (SHH, Indian hedgehog, and desert hedgehog); in this discussion, we will focus on SHH. The signaling receptor for the SHH pathway is encoded by a 7-transmembrane receptor, smoothened (SMO). In the absence of SHH, SMO signaling is inhibited by the patched (PTC) protein. This lack of signaling enables cleavage of a Gli precursor to a smaller Gli repressor, which turns off a set of genes, for example, in the developing limb or neural tube. In the presence of SHH, PTC inhibition of SMO is relieved, and signaling prevents cleavage of the Gli precursor, which generates a Gli activator that turns on genes, for example, the PTC gene itself. More details of this complex pathway can be found in many reviews and on the hedgehog Web site (http://hedgehog.sfsu.edu/).
For many years, the talpid3 chicken mutant (Figure 3) has been used to study patterning in the chick limb bud (Ede and Kelly, 1964; Francis-West et al., 1995) and has been shown to be defective in SHH signaling (Lewis et al., 1999). We have shown that talpid3 has a defect in Gli activator, where target gene expression is lost (e.g., PTC), and Gli repressor, where target genes are misexpressed (e.g., HOXD13), suggesting a common point in the SHH pathway. Using the resources and tools of chicken genomics, we have mapped and identified the defect in the talpid3 gene, identifying a novel member of the SHH signaling pathway (Davey et al., 2006). This is probably the first example of positional cloning in the chicken. Using microsatellite markers, whole genome genetic linkage mapped the gene defect to the long arm of chromosome 5. Fine-mapping of the talpid3 locus was made possible by fine-mapping genetic markers to specific haplotypes. The development of these markers was based on available EST and genome sequences and SNP resources available at the time. Examination of the Ensembl genome browser revealed 5 candidate genes in the critical region. Sequencing of full-length cDNA from both wild-type and talpid3 alleles for all 5 genes identified a genetic defect (an insertion of a single thymidine giving rise to a frameshift in the coding sequence) in the chicken ortholog of human KIAA0586, an anonymous gene with no known function. To prove that KIAA0586 was the causative gene in the talpid3 mutant, we went 1 step further and rescued the gene defect in SHH signaling in the neural tube by overexpression of a full-length cDNA delivered by electroporation (Figure 4). Again this example illustrates many of the advantages of the chick embryo system for functional characterization of vertebrate genes.
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), possibly sharing a common function; 2) using tagged proteins and talpid3 antibodies to define the cellular localization of the protein, and 3) using experiments using yeast 2 hybrid and coimmunoprecipitation coupled with proteomics analyses to define protein-protein interactions. Together, these approaches will define the molecular function of this novel protein, one that would never have been identified as a member of the SHH pathway if it were not for the genetic defect in the talpid3 chicken mutant.
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CONCLUSIONS AND FUTURE PROSPECTS |
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TOPABSTRACTINTRODUCTIONCHICKEN GENOMEIMPLICATIONS OF THE CHICKEN...CONCLUSIONS AND FUTURE PROSPECTSREFERENCES |
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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Received for publication February 15, 2007. Accepted for publication February 15, 2007.
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TOPABSTRACTINTRODUCTIONCHICKEN GENOMEIMPLICATIONS OF THE CHICKEN...CONCLUSIONS AND FUTURE PROSPECTSREFERENCES |
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